Development of genic SSR markers from transcriptome sequencing of pear buds

研究目的：基于转录组数据开发具有扩增率高和跨物种转移性的基因组编码区内的SSR（genic-SSR）标记,为梨属植物的分子系统发育关系和遗传多样性相关研究提供新的方法。创新要点：首次利用梨属植物的转录组测序（RNA-seq）数据结合M-13荧光尾巴高效率地开发了104个genic-SSR标记,并成功将其应用于梨属植物的系统发育关系研究中。研究方法：应用生物信息学软件从转录组测序数据中搜索SSR位点和设计相应引物,结合高效的M-13荧光尾巴的方法筛选多态性高的SSR标记。重要结论：转录组数据能够为梨属植物分子系统发育关系和遗传多样性研究提供新的SSR标记来源。     

Diversity arrays technology (DArT) for studying the genetic polymorphism of flue-cured tobacco (Nicotiana tabacum)

Diversity arrays technology (DArT) is a microarray-based marker system that achieves high throughput by reducing the complexity of the genome. A DArT chip has recently been developed for tobacco. In this study, we genotyped 267 flue-cured cultivars/landraces, including 121 Chinese accessions over five decades from widespread geographic regions in China, 103 from the Americas, and 43 other foreign cultivars, using the newly developed chip. Three hundred and thirty polymorphic DArT makers were selected and used for a phylogenetic analysis, which suggested that the 267 accessions could be classified into two subgroups, which could each be further divided into 2–4 sections. Eight elite cultivars, which account for 83% of the area of Chinese tobacco production, were all found in one subgroup. Two high-quality cultivars, HHDJY and Cuibi1, were grouped together in one section, while six other high-yield cultivars were grouped into another section. The 330 DArT marker clones were sequenced and close to 95% of them are within non-repetitive regions. Finally, the implications of this study for Chinese flue-cured tobacco breeding and production programs were discussed.     

Epigenetic Vestiges of Early Developmental Adversity: Childhood Stress Exposure and DNA Methylation in Adolescence

Fifteen‐year‐old adolescents (N = 109) in a longitudinal study of child development were recruited to examine differences in DNA methylation in relation to parent reports of adversity during the adolescents’ infancy and preschool periods. Microarray technology applied to 28,000 cytosine–guanine dinucleotide sites within DNA derived from buccal epithelial cells showed differential methylation among adolescents whose parents reported high levels of stress during their children’s early lives. Maternal stressors in infancy and paternal stressors in the preschool years were most strongly predictive of differential methylation, and the patterning of such epigenetic marks varied by children’s gender. To the authors’ knowledge, this is the first report of prospective associations between adversities in early childhood and the epigenetic conformation of adolescents’ genomic DNA.     

Individual Differences in Childhood Behavior Disorders Associated With Epigenetic Modulation of the Cortisol Receptor Gene

Behavioral/emotional difficulties in children are the first sign of mental health problems. These problems are however, heterogeneous. A domain that may identify homogenous subgroups is hypothalamic–pituitary–adrenal function. This study tested whether epigenetic regulation of glucocorticoid receptor gene could explain the co‐occurrence of anxiety problems in children with behavior problems. Four‐ to 16‐year‐old clinically referred children (N = 241) were measured for psychiatric symptoms, methylation of target CpG sites in blood or saliva, and morning cortisol levels in those who gave blood. Increased methylation of promoter 1F CpG sites was associated with higher vulnerability to co‐occurring internalizing symptoms and morning cortisol. The results support increasing optimism that epigenetic regulation of key neuroendocrine systems might help explain hitherto unfathomable individual differences in susceptibility to psychiatric symptom profiles.     

Determination of the genetic diversity of vegetable soybean [Glycine max (L.) Merr.] using EST-SSR markers

The development of expressed sequence tag-derived simple sequence repeats (EST-SSRs) provided a useful tool for investigating plant genetic diversity. In the present study, 22 polymorphic EST-SSRs from grain soybean were identified and used to assess the genetic diversity in 48 vegetable soybean accessions. Among the 22 EST-SSR loci, tri-nucleotides were the most abundant repeats, accounting for 50.00% of the total motifs. GAA was the most common motif among tri-nucleotide repeats, with a frequency of 18.18%. Polymorphic analysis identified a total of 71 alleles, with an average of 3.23 per locus. The polymorphism information content (PIC) values ranged from 0.144 to 0.630, with a mean of 0.386. Observed heterozygosity (H _o) values varied from 0.0196 to 1.0000, with an average of 0.6092, while the expected heterozygosity (H _e) values ranged from 0.1502 to 0.6840, with a mean value of 0.4616. Principal coordinate analysis and phylogenetic tree analysis indicated that the accessions could be assigned to different groups based to a large extent on their geographic distribution, and most accessions from China were clustered into the same groups. These results suggest that Chinese vegetable soybean accessions have a narrow genetic base. The results of this study indicate that EST-SSRs from grain soybean have high transferability to vegetable soybean, and that these new markers would be helpful in taxonomy, molecular breeding, and comparative mapping studies of vegetable soybean in the future.     

Epigenetic regulation of adipocyte differentiation and adipogenesis

It is generally agreed that adipocytes originate from mesenchymal stem cells in what can be divided into two processes: determination and differentiation. In the past decade, many factors associated with epigenetic signals have been proved to be pivotal for the appropriate timing of adipogenesis progression. A large number of coregulators at critical gene promoters set up specific patterns of DNA methylation, histone acetylation and methylation, and nucleosome rearrangement, that act as an epigenetic code to modulate the correct progress of adipocyte differentiation and adipogenesis during adipogenesis. In this review, we focus on the functions and roles of epigenetic processes in preadipocyte differentiation and adipogenesis.     

Polymorphisms in genes involved in folate metabolism as maternal risk factors for Down syndrome in China

Objective: To explore the relationship between genetic polymorphisms in methylenetetrahydrofolate reductase (MTHFR), methionine synthase reductase (MTRR), the central enzymes in folate metabolism that affects DNA methylation and synthesis, and the risk of Down syndrome in China. Methods: Genomic DNA was isolated from the peripheral lymphocytes of 64 mothers of children with Down syndrome and 70 age matched control subjects. Polymerase chain reaction and restriction fragment length polymorphism were used to examine the polymorphisms of MTHFR 677C→T, MTRR 66A→G and the relationship between these genotypes and the risk of Down syndrome was analyzed. Results: The results show that the MTHFR 677C→T polymorphism is more prevalent among mothers of children with Down syndrome than among control mothers, with an odds ratio of 3.78 (95% confidence interval (CI), 1.78～8.47). In addition, the homozygous MTRR 66A→G polymorphism was independently associated with a 5.2-fold increase in estimated risk (95% CI, 1.90～14.22). The combined presence of both polymorphisms was associated with a greater risk of Down syndrome than the presence of either alone, with an odds ratio of 6.0 (95% CI, 2.058～17.496).The two polymorphisms appear to act without a multiplicative interaction. Conclusion: MTHFR and MTRR gene mutation alleles are related to Down syndrome, and CT, TT and GG gene mutation types increase the risk of Down syndrome.     

Capillary gas chromatographic determination of dimethachlon residues in fresh tobacco leaves and cut-tobacco

Simple procedures for extraction and chromatographic determination ofdimethachlon residues in fresh tobacco leaves and cut-tobacco are described. The determination was carried out by capillary gas chromatography （GC） with electron capture detection （ECD） and confirmed by GC-MS. The mean recoveries and relative standard deviation （RSD） were 93.2%-112.9% and 3.5%-6.7%, respectively at levels ranging from 0.01 to 0.1 mg/kg. The limit of determination was 0.001 mg/kg. Tobacco samples in routine check were successfully analyzed using the proposed method.     

Normal epigenetic inheritance in mice conceived by in vitro fertilization and embryo transfer

An association between assisted reproductive technology (ART) and neurobehavioral imprinting disorders has been reported in many studies, and it seems that ART may interfere with imprint reprogramming. However, it has never been explored whether epigenetic errors or imprinting disease susceptibility induced by ART can be inherited transgenerationally. Hence, the aim of this study was to determine the effect of in vitro fertilization and embryo transfer (IVF-ET) on transgenerational inheritance in an inbred mouse model. Mice derived from IVF-ET were outcrossed to wild-type C57BL/6J to obtain their female and male line F2 and F3 generations. Their behavior, morphology, histology, and DNA methylation status at several important differentially methylated regions (DMRs) were analyzed by Morris water maze, hematoxylin and eosin (H&E) staining, and bisulfite genomic sequencing. No significant differences in spatial learning or phenotypic abnormality were found in adults derived from IVF (F1) and female and male line F2 and F3 generations. A borderline trend of hypomethylation was found in H19 DMR CpG island 3 in the female line-derived F3 generation (0.40±0.118, P=0.086). Methylation status in H19/Igf2 DMR island 1, Igf2 DMR, KvDMR, and Snrpn DMR displayed normal patterns. Methylation percentage did not differ significantly from that of adults conceived naturally, and the expression of the genes they regulated was not disturbed. Transgenerational integrity, such as behavior, morphology, histology, and DNA methylation status, was maintained in these generations, which indicates that exposure of female germ cells to hormonal stimulation and gamete manipulation might not affect the individuals and their descendents.     

Assessment of genetic diversity by simple sequence repeat markers among forty elite varieties in the germplasm for malting barley breeding

The genetic diversity and relationship among 40 elite barley varieties were analyzed based on simple sequence repeat (SSR) genotyping data. The amplified fragments from SSR primers were highly polymorphic in the barley accessions investigated. A total of 85 alleles were detected at 35 SSR loci, and allelic variations existed at 29 SSR loci. The allele number per locus ranged from 1 to 5 with an average of 2.4 alleles per locus detected from the 40 barley accessions. A cluster analysis based on the genetic similarity coefficients was conducted and the 40 varieties were classified into two groups. Seven malting barley varieties from China fell into the same subgroup. It was found that the genetic diversity within the Chinese malting barley varieties was narrower than that in other barley germplasm sources, suggesting the importance and feasibility of introducing elite genotypes from different origins for malting barley breeding in China.     

Association of hypomethylation of LINE-1 repetitive element in blood leukocyte DNA with an increased risk of hepatocellular carcinoma

Global DNA hypomethylation has been associated with increased risk for cancers of the colorectum, bladder, breast, head and neck, and testicular germ cells. The aim of this study was to examine whether global hypomethylation in blood leukocyte DNA is associated with the risk of hepatocellular carcinoma (HCC). A total of 315 HCC cases and 356 age-, sex- and HBsAg status-matched controls were included. Global methylation in blood leukocyte DNA was estimated by analyzing long interspersed element-1 (LINE-1) repeats using bisulfite-polymerase chain reaction (PCR) and pyrosequencing. We observed that the median methylation level in HCC cases (percentage of 5-methylcytosine (5mC)=77.7%) was significantly lower than that in controls (79.5% 5mC) (P=0.004, Wilcoxon rank-sum test). The odds ratios (ORs) of HCC for individuals in the third, second, and first (lowest) quartiles of LINE-1 methylation were 1.1 (95% confidence interval (CI) 0.7–1.8), 1.4 (95% CI 0.8–2.2), and 2.6 (95% CI 1.7–4.1) (P for trend <0.001), respectively, compared to individuals in the fourth (highest) quartile. A 1.9-fold (95% CI 1.4–2.6) increased risk of HCC was observed among individuals with LINE-1 methylation below the median compared to individuals with higher (>median) LINE-1 methylation. Our results demonstrate for the first time that individuals with global hypomethylation measured in LINE-1 repeats in blood leukocyte DNA have an increased risk for HCC. Our data provide the evidence that global hypomethylation detected in the easily obtainable DNA source of blood leukocytes may help identify individuals at risk of HCC.     

Clones identification of Sequoia sempervirens (D. Don) Endl. in Chile by using PCR-RAPDs technique

A protocol of polymerase chain reaction-random amplified polymorphic DNAs (PCR-RAPDs) was established to analyse the gene diversity and genotype identification for clones of Sequoia sempervirens (D. Don) Endl. in Chile. Ten (out of 34) clones from introduction trial located in Voipir-Villarrica, Chile, were studied. The PCR-RAPDs technique and a modified hexadecyltrimethylammonium bromide (CTAB) protocol were used for genomic DNA extraction. The PCR tests were carried out employing 10-mer random primers. The amplification products were detected by electrophoresis in agarose gels. Forty nine polymorphic bands were obtained with the selected primers (BG04, BF07, BF12, BF13, and BF14) and were ordered according to their molecular size. The genetic similarity between samples was calculated by the Jaccard index and a dendrogram was constructed using a cluster analysis of unweighted pair group method using arithmetic averages (UPGMA). Of the primers tested, 5 (out of 60) RAPD primers were selected for their reproducibility and high polymorphism. A total of 49 polymorphic RAPD bands were detected out of 252 bands. The genetic similarity analysis demonstrates an extensive genetic variability between the tested clones and the dendrogram depicts the genetic relationships among the clones, suggesting a geographic relationship. The results indicate that the RAPD markers permitted the identification of the assayed clones, although they are derived from the same geographic origin. Project (No. CONICYT-FONDEF PROYECT D01 I 1008) supported by the National Commission of Science and Research of Chile     

Study on pig growth hormone gene polymorphisms in western meat-type breeds and Chinese local breeds

Chinese Meishan and Jiangquhai pigs are two of the most prolific pigs in the world, but their growth rate is lower than that of Duroc, Landrace and Pietrain pigs. It is suggested that growth rate is regulated by growth hormone. The objective of the current study was to analyze the porcine growth hormone (pGH) gene polymorphisms based on the polymerase chain reaction restriction fragment-length polymorphism method (PCR-RFLP) for three western meat-type breeds (Duroc, Landrace and Pietrain) and two local Chinese pigs (Meishan and Jiangquhai). Five polymorphic restriction sites were detected with the ApaI, MspI, BspI and HhaI restriction enzymes in two amplified fragments (605 bp, -119 to +486; 506 bp, +206 to +711). Breed difference was found only in the 506 bp fragment. There was no difference in allelic frequencies of BspI and HhaI restriction sites among the five breeds (P>0.05). Landrace and Meishan pigs lacked allele G3 of MspI site. The allele G3 frequency of restriction MspI site of the 506 bp fragment in Pietrain pigs was higher than that in Duroc and Jianquhai pigs (P<0.001). For ApaI site, the Meishan pigs lacked allele G1; no difference was found in allelic frequencies among Pietrain, Duroc, Landrace and Jiangquhai pigs (P>0.05). This new and rapid PCR-RFLP typing method is an attractive tool for analysis of porcine growth hormone gene restriction sites. The differences in MspI and ApaI restriction sites may explain the growth difference between the foreign meat-type breeds above mentioned and local Chinese pigs.     

Study on pig growth hormone gene polymorphisms in western meat-type breeds and Chinese local breeds

INTRODUCTIONGrowthhormone (GH)isapeptidehormonewhichregulatesgrowthandvariousmetabolicac tivities (Sterle,1 995;Yuan ,1 996) .InjectionsofGHintogrowingpigsincreasedgrowthrateoftheanimalsandthepercentageofmuscle ,andwhilefataccretionwasdecreased (Bonneau ,…     

基于杨梅基因组鸟枪法测序开发的107个SSR标记及其在品系鉴定中应用

研究目的：开发多态性高的基因组简单重复序列（SSR）标记,为杨梅遗传多样性、遗传图谱构建及品种鉴定相关研究奠定基础。 创新要点：从杨梅全基因组鸟枪法测序数据中新开发了107个SSR标记,并应用于品种间遗传多样性分析及品系鉴定。 研究方法：应用生物信息学软件从基因组测序数据中搜索SSR位点并设计相应引物,添加通用的M13尾巴和荧光标识筛选多态性高的SSR标记。 重要结论：开发的107个基因组SSR标记可以广泛应用于杨梅种质资源和遗传育种研究,鉴定出三个杨梅新品系。     

Analysis of genetic diversity in banana cultivars (Musa cvs.) from the South of Oman using AFLP markers and classification by phylogenetic, hierarchical clustering and principal component analyses

Banana is an important crop grown in Oman and there is a dearth of information on its genetic diversity to assist in crop breeding and improvement programs.This study employed amplified fragment length polymorphism(AFLP) to investigate the genetic variation in local banana cultivars from the southern region of Oman.Using 12 primer combinations,a total of 1094 bands were scored,of which 1012 were polymorphic.Eighty-two unique markers were identified,which revealed the distinct separation of the seven cultiva...     

Development and testing of an antitobacco school-based curriculum for deaf and hard of hearing youth

A tobacco use prevention curriculum tailored for deaf/hard of hearing youth was tested using a quasi-experimental design. Two schools for the deaf received the curriculum; two served as noncurriculum controls. Surveys assessed changes in tobacco use, tobacco education exposure, and tobacco-related attitudes and knowledge among students in grades 7-12 over 3 school years (n = 511-616). Current (past month) smoking decreased significantly at one intervention school (23% to 8%,p = .007), and current smokeless tobacco use at the other (7.5% to 2.5%, p = .03). Tobacco education exposure and antitobacco attitudes and knowledge increased significantly at one or both intervention schools. At one control school, reported tobacco education exposure decreased (p < .001) and antitobacco attitudes increased (p = .01). The results indicate that the curriculum increased perceived tobacco education exposure and significantly affected tobacco-related practices, attitudes, and knowledge.     

Early social communication development in infants with autism spectrum disorder

Social-communication differences are a robust and defining feature of autism spectrum disorder (ASD) but identifying early points of divergence in infancy has been a challenge. The current study examines social communication in 9- to 12-month-old infants who develop ASD (N = 30; 23% female; 70% white) compared to typically developing (TD) infants (N = 94, 38% female; 88% white). Results demonstrate that infants later diagnosed with ASD were already exhibiting fewer social-communication skills using eye gaze, facial expression, gestures, and sounds at 9 months (effect size: 0.42–0.89). Moreover, three unique patterns of change across distinct social-communication skills were observed within the ASD group. This study documents that observable social-communication differences for infants with ASD are unfolding by 9 months, pointing to a critical window for targeted intervention.     

Longitudinal Associations Among Child Maltreatment,Resting Frontal Electroencephalogram Asymmetry,and Adolescent Shyness

Child maltreatment is linked to distinct neurophysiological patterns and social‐emotional vulnerability. Relations among maltreatment, relative resting frontal alpha asymmetry, shyness, and psychopathology were examined prospectively. Adolescent girls (age 14–16) who experienced child maltreatment (N = 55) were compared to nonmaltreated controls (N = 25), and returned for 6‐ and 12‐month follow‐ups. Among participants exhibiting relative right frontal asymmetry, maltreated adolescents reported higher shyness than controls at Time 1. Low‐stable and high‐stable shyness trajectories were observed for maltreated participants. Compared to low shy, participants in high‐shy trajectory reported at Time 3: higher neuroticism and generalized anxiety; and lower extraversion if they also exhibited relative right frontal asymmetry. Thus, right frontal brain activity and shyness are involved in social‐emotional vulnerability of adolescents who experienced child maltreatment.     

Trajectories of Ethnic‐Racial Discrimination Among Ethnically Diverse Early Adolescents: Associations With Psychological and Social Adjustment

Using longitudinal data, the authors assessed 585 Dominican, Chinese, and African American adolescents (Grades 6–8, M_age at W1 = 11.83) to determine patterns over time of perceived ethnic‐racial discrimination from adults and peers; if these patterns varied by gender, ethnicity, and immigrant status; and whether they are associated with psychological (self‐esteem, depressive symptoms) and social (friend and teacher relationship quality, school belonging) adjustment. Two longitudinal patterns for adult discrimination and three longitudinal patterns for peer discrimination were identified using a semiparametric mixture model. These trajectories were distinct with regard to the initial level, shape, and changes in discrimination. Trajectories varied by gender and ethnicity and were significantly linked to psychological and social adjustment. Directions for future research and practice are discussed.